[Abstract] Objective To study the mechanism of polymorphism of Car2 and Gpi1 genes at single nucleotide polymorphism (SNP) level. Methods Car2 and Gpi1 genes were analyzed based on DNA, cDNA and protein polypeptide. Results For Car2, three SNPs were observed between the two haplotypes in the genome DNA and cDNA, which were C(T), G(C) of exon 2 and A(G) of exon 7. And for the protein polypeptide the interchange of Gln/His at position 38 were detected, corresponding to G（C）of exon 2. For Gpi1, T(C) of exon 9 and A(G) of exon 18 were observed between the two haplotypes in cDNA. For the protein polypeptide Phe/Leu at position 247 was detected, corresponding to T(C) of exon 9. And none was detected in the genome DNA. Conclusion The interchanges of Gln/His at position 38 and Phe/Leu at position 247 might provide the basis for Car2a/b and Gpi1a/b haplotypes respectively.